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rase (version 0.2-2)

Range Ancestral State Estimation for Phylogeography and Comparative Analyses

Description

The rase package primarily implements the Range Ancestral State Estimation for phylogeography described in Quintero, I., Keil, P., Jetz, W., Crawford, F. W. 2015 Historical Biogeography Using Species Geographical Ranges. Systematic Biology. doi: 10.1093/sysbio/syv057. It also includes Bayesian inference of ancestral states under a Brownian Motion model of character evolution and Maximum Likelihood estimation of rase for n-dimensional data. Visualizing functions in 3D are implemented using the rgl package.

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Version

Install

install.packages('rase')

Monthly Downloads

12

Version

0.2-2

License

GPL (>= 2)

Maintainer

Ignacio Quintero

Last Published

August 13th, 2015

Functions in rase (0.2-2)

data.for.3d

Transform Output for 3D Plotting
bm_loglik_tree

Point Brownian motion tree likelihood
poly_center

Calculate the Polygon Center
phylo.3d

Plots a Phylogenic Tree in 3D
bm_est_sigma2

Estimate Sigma and Sigma Variance
bm_loglik_trio

Fast likelihood of a 2-dimensional point with two daughters and one ancestor nodes
ranges.like.bm

n-dimensional Maximumn Likelihood of Range Brownian Motion
point.like.bm

n-dimensional Maximum Likelihood of Point Brownian Motion
rase-package

Range Ancestral State Estimation
bm_propose_trio

MCMC proposal for a 2-dimensional point with two daughters and one ancestor nodes
rase

Bayesian Range Ancestral State Estimation of Polygons
add.dens

Plot the Posterior Density for each Ancestor in 3D Space
tree.slice

Identify Tree Branches That Intersect With a Given Time Slice.
bm_ase

Bayesian Ancestral State Estimation with Points
bm_loglik_ancestors

Likelihood of ancestors using points
add.polygons

Plot the Distributions for the Phylogenetic Tips in 3D
bigauss_pdf

Bivariate Gaussian PDF
bm_loglik_tree_constrained

Range Brownian motion tree likelihood
bm_loglik_ancestors_poly

Fast likelihood of ancestors using polygons
bm_loglik_duo

Likelihood of a 2-dimensional point with one daughter and one ancestor nodes
name.poly

Name & Order Polygons According to the Phylogeny
shape.to.rase

Transform a Shapefile into owin.object Format
rase_data

Psophia Data Used for rase Package
rase.slice

Ancestral State Estimation At Any Given Time Slice
random_rase3d

Apply rase to Randomly Generated Data
post.mcmc

Post-MCMC Handling
bm_propose_duo

MCMC proposal for a 2-dimensional point with one daughter and one ancestor nodes